From cef29005a5f1116d0fc4955d600b9c85c44344a5 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Tue, 18 Nov 2025 15:30:06 +0100
Subject: [PATCH] debug url reading

---
 pkg/obiformats/universal_read.go           |  1 -
 pkg/obitax/taxonset.go                     |  1 -
 pkg/obitools/obiconvert/sequence_reader.go | 10 +++++++++-
 3 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/pkg/obiformats/universal_read.go b/pkg/obiformats/universal_read.go
index b6c5196..62e967e 100644
--- a/pkg/obiformats/universal_read.go
+++ b/pkg/obiformats/universal_read.go
@@ -112,7 +112,6 @@ func ReadSequencesFromFile(filename string,
 	var err error
 
 	options = append(options, OptionsSource(obiutils.RemoveAllExt((path.Base(filename)))))
-
 	file, err = obiutils.Ropen(filename)
 
 	if err == obiutils.ErrNoContent {
diff --git a/pkg/obitax/taxonset.go b/pkg/obitax/taxonset.go
index 44288ec..935e711 100644
--- a/pkg/obitax/taxonset.go
+++ b/pkg/obitax/taxonset.go
@@ -234,7 +234,6 @@ func (taxo *TaxonSet) AsPhyloTree(root *TaxNode) (*obiphylo.PhyloNode, error) {
 	nodes := make(map[*string]*obiphylo.PhyloNode, taxo.Len())
 	tsi := taxo.Iterator()
 
-	log.Warnf("Coucou")
 	for tsi.Next() {
 		taxon := tsi.Get()
 		id := taxon.Node.Id()
diff --git a/pkg/obitools/obiconvert/sequence_reader.go b/pkg/obitools/obiconvert/sequence_reader.go
index bc2759c..c985a18 100644
--- a/pkg/obitools/obiconvert/sequence_reader.go
+++ b/pkg/obitools/obiconvert/sequence_reader.go
@@ -19,6 +19,13 @@ func ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
 	list_of_files := orderedset.NewOrderedSet()
 	for _, fn := range filenames {
 
+		if strings.HasPrefix(fn, "http://") ||
+			strings.HasPrefix(fn, "https://") ||
+			strings.HasPrefix(fn, "ftp://") {
+			list_of_files.Add(fn)
+			continue
+		}
+
 		err = filepath.Walk(fn,
 			func(path string, info os.FileInfo, err error) error {
 				var e error
@@ -147,7 +154,6 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 		if err != nil {
 			return obiiter.NilIBioSequence, err
 		}
-
 		switch CLIInputFormat() {
 		case "fastq", "fq":
 			reader = obiformats.ReadFastqFromFile
@@ -178,8 +184,10 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 				nreader,
 				opts...,
 			)
+
 		} else {
 			if len(list_of_files) > 0 {
+
 				iterator, err = reader(list_of_files[0], opts...)
 
 				if err != nil {